Genome sequencing services are currently available to and being utilized by physicians and their patients in both research and clinical settings. However, the widespread availability and use of genome sequencing in the practice of clinical medicine is imminent. In the very near future, sequencing of individual genomes will be inexpensive and ubiquitous, and patients will be looking to the medical establishment for interpretations, insight and advice to improve their health.

Developing standards and procedures for the use of sequencing information in clinical medicine is an urgent need with numerous obstacles to integrity and storage of sequencing data, interpretation, and responsible clinical integration. The MedSeq Project seeks to develop a process to integrate genome sequencing into clinical medicine and explore the impact of doing so.

We believe that whole genome sequencing (WGS) will be used in many ways, including two distinct and complementary situations. In generally healthy patients, physicians will use the results of WGS to derive insight into future health risks and inform prevention and surveillance efforts, a category we refer to as General Genomic Medicine. In patients presenting with a family history or symptoms of a disease, physicians will use the results of WGS to interrogate particular sets of genes known to be associated with the disease in question, a category we refer to as Disease-Specific Genomic Medicine.

A research protocol to explore General and Disease-Specific Genomic Medicine

Our research team of over 50 investigators, staff and expert consultants spent over a year designing a protocol to explore the integration of WGS in clinical medicine. We are recruiting and enrolling 10 primary care physicians (PCPs) and 100 of their generally healthy middle-aged patients ages 40-65 to evaluate the use of General Genomic Medicine, and 10 cardiologists and 100 of their patients with hypertrophic or dilated cardiomyopathy to evaluate the use of Disease-Specific Genomic Medicine. We are randomizing physicians and their patients within each of the above models to receive clinically meaningful information derived from WGS plus a family history assessment versus current standard of care plus a family history assessment without the use of WGS.

Our team designed a mixed-methods approach, utilizing quantitative surveys and qualitative methods, to examine preferences and motivations of physicians and patients enrolled, evaluate the flow and utilization of genomic information within the clinical interactions, and assess understanding, behavior, medical consequences and healthcare costs associated with the use of WGS in these models of medical practice.

Delivering a genome sequencing information to physicians

Our team designed a process to obtain WGS on the patients randomized into those groups, interpret variants and deliver a Genome Report to the patients’ physicians. The MedSeq Project Genome Report includes highly penetrant Mendelian mutations, highly penetrant recessive carrier states, pharmacogenomic associations, and blood group. In addition, a Cardiac Risk Supplement contains more exploratory genetic information related to cardiovascular disease risk and treatment. The Genome Report is delivered to the physician along with patient-entered family history information from the US Surgeon General’s Family History Tool. The physician reviews the results from the Genome Report and/or family history assessment with the patient in his or her own clinic. Our research team “observes” these interactions via audio recording. After the disclosure encounter, the Genome Report is sent to the patient’s electronic medical record using the GeneInsight Clinic® Program through the Partners Laboratory for Molecular Medicine.

Physician support

The team designed an educational module for the enrolled physicians to complete prior to disclosing WGS results to their patients. The module consists of 2 in-person lectures and 4 hours of online coursework and was accredited by the Partners HealthCare System for a maximum of 6.5 AMA PRA Category 1 Continuing Medical Education Credit(s)™. In addition, we created a MedSeq Project Genome Resource Center (GRC), staffed with medical geneticists and genetic counselors, for the physicians to consult regarding their patients’ Genome Report and/or family history information.

Project status

We obtained Institutional Review Board approval in August 2012. We enrolled 11 PCPs, 9 cardiologists, and 202 of their patients. All 100 Genome Reports have been delivered to enrolled physicians and their patients.

Three total MedSeq participants randomized to the control group will have the opportunity to have their whole genome sequenced as part of the MedSeq lottery after they have completed their 6-month surveys. We have drawn 2 of the 3 lottery participant winners and their blood has been collected and the sequence is being analyzed.

We have continued our work on the extension phase of the study, which includes: recruitment of additional African American participants into the sequencing arm and re-phenotyping of participants with monogenic findings. We have enrolled six new African American study participants.

This initiative will significantly accelerate the use of genomics in clinical medicine by creating and safely testing novel methods for integrating information from WGS into physicians’ care of patients.

To learn more about this study, or to reach a representative for further comment, please contact Dr. Green, or Carrie Blout, MS, CGC, Genetic Counselor and Project Manager for the MedSeq Project.

The BabySeq Project: Genomic Sequencing for Childhood Risk and Newborn Illness (U19 HD077671) is a first-of-its-kind randomized clinical trial designed to examine how best to use genomics in clinical pediatric medicine by creating and safely testing methods for integrating sequencing into the care of newborns.

Currently, the risks and benefits of genomic sequencing for newborns are not well understood. All newborns receive “Newborn Screening,” a state-mandated heel stick blood test shortly after birth in order to screen for approximately 30 heritable, treatable conditions such as blood, endocrine, and metabolic disorders. Genomic sequencing has the potential to allow for significantly more extensive screening of disorders that newborns could be at risk for developing during childhood. Earlier diagnosis of these conditions could in turn lead to specific screening, surveillance and treatment options, allowing for more personalized and preventative healthcare.

The extent to which genomic information could benefit or harm newborns and their families remains unclear. Despite this uncertainty, the use of genomic technology is continuing to expand throughout medicine. It is therefore important to study the impact of genomic screening in a safe and controlled manner, before market forces outpace our understanding of the implications of this technology.

In a pilot study conducted at BWH that helped inform the design of the BabySeq Project, parents of healthy newborns were asked on the BWH post-partum unit how interested they would be in genome screening of their newborn if available through a research study. We also presented a subset of these parents with descriptions of possible results whichcould be detected by genome sequencing. These parents were then asked hypothetically which results they would want to receive about their newborn. The vast majority of parents, 82.7 percent, reported being “somewhat” (36 percent), “very” (28 percent), or “extremely” (18 percent) interested in newborn genomic testing.

The BabySeq Project received Institutional Review Board approval in Spring 2015 and enrollment is now underway. The study is enrolling 240 healthy newborns and their families from BWH and 240 newborns and their families from the Neonatal Intensive Care Unit (NICU) at BCH. Each infant is randomized (50:50) to receive genomic sequencing or to a control group. All babies receive state-mandated conventional newborn screening and a family history report, while babies in the sequencing arm also receive a genomic sequencing report. This report contains information about known pathogenic or likely pathogenic (e.g. disease-causing) variants associated with childhood-onset conditions identified in the infant. It may also contain information on “pharmacogenomic” variants, genetic changes that could affect response to certain medications, and the baby’s blood type. Babies in the sequencing arm who have, or develop, health conditions that may have an underlying genetic cause may also receive an “Indication-Based Analysis” that can re-examine the baby’s sequencing information, with a specific focus on genes that have previously been associated with the baby’s specific health condition.

In order to monitor the long-term impact of the genomic information returned to families, parents enrolled in the study are asked to complete four surveys over the course of the first year of enrollment. These surveys ask questions about how parents have been feeling, their family relationships, genetics knowledge, and the perceived utility of the information they receive. We are examining if there are marked differences between the families who receive genomic information and the families who receive standard of care.

We are also enrolling and surveying pediatricians and other doctors involved in the care of enrolled babies to examine how this information may be impacting a child’s medical care.

We hope that this project will provide valuable and unparalleled data to be used to integrate genomic information from newborns into clinical pediatric care.

The BabySeq project is part of a consortium called Newborn Sequencing In Genomic medicine and public HealTh, dubbed NSIGHT. Along with projects at Baylor College of Medicine, UNC School of Medicine, UCSF School of Medicine, UCSD Rady Children’s Institute for Genomic Medicine, and Children's Mercy Kansas City, the consortium has been granted $25M over a five year period to gather critical research on newborn sequencing. The NSIGHT consortium investigates three clinical scenarios: diagnostic (using genome sequencing to find the specific genetic causes of congenital anomalies or unexplained illnesses in babies admitted to the hospital early in life); preventative (using genome sequencing to screen healthy newborns for preventable or treatable conditions of childhood that genetic sequencing could detect or help confirm); and predictive (using genome sequencing to explore the entire genome of the child, as a resource for health care throughout the course of the child’s life). Critical data gathered from the NSIGHT projects will help to address technical, medical, behavioral and economic questions surrounding newborn sequencing – and ultimately, will aid in the development of best clinical practices and provide guidance on the implementation of sequencing in newborns.

The rapid identification of genetic risk factors for common, complex diseases poses great opportunities and challenges for public health. Genetic information is increasingly being utilized as part of commercial efforts, including personal genomic testing, to provide consumers with genetic risk information related to common diseases. Few empirical data have been gathered to understand the characteristics of consumers, the psychological, behavioral, and health impact, and the ethical, legal, and social issues associated with personal genomic testing services.

In the NIH-funded Impact of Personal Genomics (PGen) Study, we surveyed consumers of two U.S. companies that provide personal genetic testing—23andMe and Pathway Genomics—to determine consumers’ reactions to genetic risk information for common diseases of interest, including heart disease, diabetes, Alzheimer’s disease, arthritis, and breast, colon, lung, and prostate cancers. This study utilizes third-party data collection and analysis procedures to enable an independent consideration of the benefits and risks of personal genomic testing. With participants’ permission, 23andMe and Pathway Genomics also provided researchers with individual-level genetic risk information, which was subsequently linked to participants' longitudinal survey responses. A total of 1,648 participants provided survey data at baseline, of which 1,489 were eligible for follow-up. Of these, survey data was collected from 1,046 participants at 2-week follow-up, and 1,042 participants at 6-month follow-up. Over 900 participants completed all 3 surveys, and 1,155 participants completed at least one follow-up survey, resulting in a large and diverse cohort for longitudinal investigations into the impact of personal genomic testing.

To implement this research, we have assembled an interdisciplinary team of experts with backgrounds in medicine, genetic testing policy and practice, health communication, genetic counseling, health psychology, health law, bioethics, and web survey design. Our aims are as follows: 1) to describe who seeks personal genomic testing and why, by collecting information on demographics, motivations for seeking testing, and understanding of genetics; 2) to describe the impact of personal genomic testing, including psychological impact, risk perceptions and comprehension, and personal utility of services; and 3) to assess what consumers do with their genetic information in the domains of health behaviors, insurance changes, information seeking, and communication with family and health care providers. This study will produce results that can be translated into recommendations to guide practice and policy in this rapidly emerging area.

Alzheimer’s disease (AD) clinical trials have traditionally tested potential treatments for individuals with symptoms of dementia, but the discovery of AD biomarkers has dramatically altered this approach. Trials such as the Anti-Amyloid in Asymptomatic Alzheimer’s Study, or A4 Study, are now focusing on enrolling cognitively normal participants who have biomarkers suggestive of “preclinical AD,” in order to delay the onset of cognitive impairments. This goal presents two questions of critical importance to both the validity and safety of these trials, and the successful translation of their results into clinical practice: (1) Will individuals’ knowledge of their biomarker status bias cognitive outcomes? (2) Will such knowledge prompt beneficial behavior changes or cause adverse psychological and social consequences?

REVEAL-SCAN: Risk Evaluation and and Education of Alzheimer's Disease - the Study of Communicating Amyloid Neuroimaging (RF1 AG047866) is the first multi-site, randomized clinical trial to examine the impact of learning amyloid imaging results in cognitively normal individuals, and its goal is to answer these questions.

If simply learning that one is biomarker positive causes a person to perform worse on cognitive testing, then primary outcomes data of AD trials may not be valid. Moreover, since amyloid imaging received FDA approval for use in cognitively impaired individuals, our preliminary studies show that clinical investigators want guidance on whether and how to disclose amyloid imaging results, not only to these individuals, but also to cognitively normal older individuals.

In this study, risk communication protocols will be developed and implemented for communicating amyloid PET brain imaging results. Then, 270 cognitively normal individuals (approximately 25% African American), aged 65-80, will be recruited and randomized to receive their amyloid scan results or not, resulting in subjects whose scan results are disclosed or not and subjects whose scans are amyloid positive or not. Apolipoprotein (APOE) genotyping with oversampling of ε4+ individuals will be used to enrich the enrollment sample, such that roughly half of those scanned will be amyloid positive and half will be amyloid negative. The primary neuropsychological outcome will be the ADCS Preclinical Alzheimer Cognitive Composite (ADCS-PACC) and the primary psychological outcome for psychological distress will be the Impact of Events Scale (IES).

The core team that will conduct this project has worked together for over ten years on the NIH-funded REVEAL Study (R01 HG02213) trials that have studied risk estimation, risk communication and the disclosure of APOE genotype for risk of AD. Our aims are as follows: 1) to determine whether disclosure of elevated brain amyloid will bias ADCS-PACC test results; 2) to determine whether disclosure of elevated brain amyloid will cause psychological distress; and 3) to explore how learning amyloid imaging disclosure will impact preventative health behaviors, advance planning for health (e.g. long-term care insurance decisions) and well-being (e.g. stigma, quality of life and relationships).

Genomic sequencing, including whole genome sequencing (WGS) and whole exome sequencing (WES), are available to and being utilized by physicians and their patients in both research and clinical settings. Thousands of patients have received genomic sequencing with the goal of establishing diagnoses for rare or genetically heterogeneous disorders, a process that previously would have required multiple individual genetic tests performed over long periods of time and at a substantial cost. Beyond its diagnostic utility, there is hope that genomic sequencing, when performed in ostensibly healthy individuals, will be a key tool in the development of a more personalized and preventative model of medical care.

The use of genomic sequencing in healthy populations to screen for disease variants is conceptually very different from anything practiced today in medical genetics. Instead of using genomic technology in the hopes of identifying a cause for a specific condition, genomic sequencing in healthy individuals would follow a model of "predispositional" genomic testing. Unlike many epidemiologic studies in genetics and genomics, this model envisions results being returned in a readily understandable report to patients and their clinicians as part of the patient’s regular care. Identification of rare genetic variants associated with significantly increased risks for certain cardiac events or cancers could allow for preemptive clinical management and prevention of disease. Genomic sequencing of healthy individuals could grow to resemble current population-based preventative screening measures, such as newborn screening or the use of colonoscopy after age 50, which have been integrated into clinical practice to identify uncommon diseases.

Despite the promise of genomic sequencing for personalized medicine, there remain significant challenges and concerns that must be addressed. Some consider the utilization of genomic sequencing in healthy individuals to be controversial; the short and long-term outcomes of providing genomic sequencing information to healthy adults are not known and are of great interest.

In the PeopleSeq Consortium, we are conducting a longitudinal study of healthy adults by surveying those who plan to, or have already received, their own genomic sequence information through various commercial and research avenues that follow different return of results models. The PeopleSeq Consortium enables us to collect valuable empirical data on the medical, behavioral and economic impact of performing genomic sequencing in healthy adults. To accomplish this, we have drawn upon our prior experience in designing and implementing rigorous studies of the outcomes of genetic testing and results disclosure, including the Impact of Personal Genomics (PGen) Study and the MedSeq Project.

To view preliminary data from the PeopleSeq Consortium, please click here and here.

To learn more about the study please contact Wendi Betting, Project Manager for the PeopleSeq Consortium.

Our econogenomics working group brings together a diverse set of researchers with a variety of clinical and scientific expertise. Together, our mission is to understand the economic impact of translating genomic advances into clinical practice. Genomic medicine has the potential to revolutionize patient care. Yet, major questions remain about the value it provides and its impact overall health care expenditures. Advocates hope that genomic medicine will help control expenditures by streamlining diagnostic processes, informing selection and dosing of treatments, and identifying at‐risk individuals to facilitate targeted prevention. The price of genomic medicine, however, remains high relative to most other tests; and some tests, such as genomic sequencing may identify secondary findings that initiate a cascade of confirmatory and follow‐up testing that may not be warranted. These uncertainties pose major barriers to the practice of genomic medicine, making many payers reluctant to cover services.

Working group MemberS

Mission

To assess the economic aspect of translating genomic medicine into clinical practice.

Cores

Economic Modeling: Our economic modeling core, led by Dr. Ann Wu, uses a variety of modeling approaches to project the medical and financial consequences of genomic medicine, including the use of pharmacogenomic testing to inform medication choices and the use of sequencing as an adjunct to standard newborn screening.

Areas of Focus

Pharmacogenomics: Pharmacogenomics is the study of how a person’s genetic makeup affects how medications and medication doses are likely to work best for a particular person or which individuals are more likely to suffer adverse consequences. Pharmacogenomic tests have the potential to improve resource allocation by improving targeting of treatments so that individuals at risk of having adverse responses to medications or not responding to medications can avoid them, thereby reducing healthcare costs. With thousands of pharmacogenomic tests under development and many becoming available for clinical use, it is becoming increasingly important to understand the costs and benefits of these tests so that their potential for widespread use can be critically evaluated in ways that optimize their usefulness.

Genome and Exome Sequencing: Genome and exome sequencing has increasing utility for diagnosing disease and informing treatment decisions. With costs decreasing rapidly, many thought leaders believe that such sequencing will become commonplace, even among healthy individuals. Yet, the benefits and harms of integrating sequencing into the care of many populations are still unclear, as are the cost implications. Capitalizing on our experiences with high-profile clinical trials such as the MedSeq Project and BabySeq Project and our strong relationship with the Laboratory for Molecular Medicine, our group is using a combination of modeling and clinical studies to examine the costs and consequences of integrating genome and exome sequencing into a variety of clinical settings.

Reimbursement: Given the uncertainties about the health and financial impact of many genomic tests, payers are often reluctant to cover genomic services. Our group has ongoing efforts to engage with payers to educate them about how genomic tests work and their potential consequences for patients, physicians, and health care systems. As part of this dynamic, we also aim to better understanding the payer perspective to direct future research in ways that can reduce uncertainties and improve their decision making about reimbursement.

The Risk Evaluation and Education for Alzheimer’s Disease (REVEAL) Study

(R01 HG002213)

Principal Investigator: Robert C. Green

The Risk Evaluation and Education for Alzheimer’s Disease (REVEAL) study has made important contributions to the scientific understanding of the emotional, behavioral, and health-related impact of disclosing genetic risk for Alzheimer’s disease. The most recent REVEAL trial seeks to build on these past findings by studying individuals with mild memory problems and their caregivers. Data from this trial will inform ethical, social and policy issues in predictive genetic testing in Alzheimer’s disease and other common, complex diseases. These issues are increasingly important as genetic testing becomes more widely available, and there is a desire to identify individuals at earlier stages of memory loss among researchers and clinicians.

The study has been funded by the NHGRI since 1999 (R01 HG02213) and is currently in its fourth funding cycle. The project is an ongoing series of multi-site randomized controlled clinical trials that provide empirical data to address these ethical, social and translational issues in genetic susceptibility testing for common diseases. Such work has become increasingly important given the expansion of genome-wide association studies identifying genetic risk factors for common diseases and corresponding efforts to commercialize genetic testing using these markers. Our paradigm for these trials is disclosure of Apolipoprotein E (APOE) genotype as part of a risk assessment for Alzheimer’s disease (AD) to unaffected individuals. In previous funding cycles we have enrolled over 1100 participants in three separate trials, and we have been highly productive in analyzing many aspects of the psychological impact and health behavior changes of receiving genetic risk information.

REVEAL IV is the first translational genetics study to focus upon the situation where mild early symptoms of a disease (phenotype) and known genetic risk marker (genotype) information can be used together to produce more imminent risk projections. We have developed genetic specific risk curves for patients with Mild Cognitive Impairment, a condition where the APOE e4 allele is associated with more rapid progression to AD and differential response to certain pharmacological treatments. We are examining the impact of “imminent risk assessment” (i.e., risk of conversion to AD within three years) in these individuals and their care partners.

Additionally, as part of the REVEAL Long-Term Follow-Up Study, we are systematically studying the long-term psychological impact and health behavior changes in participants who learned their APOE genotype in earlier cycles of the REVEAL Study, some of whom were enrolled as early as 2000.

Reports from the REVEAL Study have explored the quantitative development of risk estimates from epidemiological studies and in different ethnic groups, the emotional impact of disclosing risk information, the reasons people seek genetic risk information, issues in self-perception of risk and how these change with genetic testing, the degree to which participants recall their test results or discuss them with others, the degree to which genetic testing affects insurance purchasing, and the degree to which genetic testing alters health behaviors.

Further data from the REVEAL IV Study will help inform policy and practice regarding the use of genetic risk information for common, complex diseases.

This NIH-funded study explores how different types of information derived from whole genome sequencing may affect demands for additional clinical services. Physicians of the Partners HealthCare System will be presented hypothetical whole genome sequencing reports and asked to rate the likelihood that they would seek more information. Satisfaction with information and the process of disclosure will also be assessed. The findings of this study will provide valuable insight about how best to present information generated by whole genome sequencing to optimize patient care and minimize the unnecessary use of limited healthcare resources.

To learn more about this study, or to reach a representative for further comment, please contact Dr. Christensen or Dr. Green.